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Frequently used modules

  • Coordinate manipulation and analysis / corman
  • Energy commands / energy
  • Non-bonded options / nbonds
  • Minimization / minimiz
  • Molecular dynamics / dynamc
  • Constraints and restraints / cons
  • Time series and correlation functions / correl
  • Atom selections / select

Modules in alphabetical order

abpo / ace / adumb / afm / analys / apbs / aspenr / aspenrmb / axd / block / cadpac / cca / cff / cfti / changelog / charmm / charmmrate / cheq / cmake / commands / cons / consph / corman / correl / corsol / cross / crystl / csa / dcor / denbias / developer / diesel / dimens / dims / domdec / drude / dynamc / eds / eef1 / emap / energy / ensemble / epmf / ewald / facts / fitcharge / fitparam / flucq / fmm / fourd / fren / g09 / galgor / gamess / gamess-uk / gamus / gbim / gbmv / gbsw / genborn / gnn / gopair / gpu / graphx / grid / hbonds / hbuild / hqbm / images / install / intcor / io / larmord / lonepair / lupopt / mc / mcma / minimiz / miscom / mmff / mmff_params / mmfp / mmpt / mndo97 / molvib / monitor / mrmd / ms-evb / mscale / mtp / mtpl / mts / nbonds / nmr / nose / nwchem / openmm / overlap / parallel / parmfile / pbeq / pdetail / pert / perturb / phmd / pimplem / pipf / pnm / preflx_list / prefx / pressure / primo / proto / qchem / qmmm / qturbo / qub / random / rdc / rdfsol / repdstr / replica / rism / rtop / rush / rxncons / sasa / sbound / scalar / sccdftb / scpism / select / sgld / shapes / shell / ssnmr / stringm / struct / subst / support / tamd / test / testcase / tmd / torque / tpcntrl / tps / trek / umbrel / usage / valbond / vibran / zerom

Complete list of modules

  • Adaptively Biased Path Optimization (ABPO) Method / abpo
  • Analytical Continuum Solvent (ACS) Potential / ace
  • Adaptive Umbrella Sampling Module / adumb
  • The AFM Module of CHARMM / afm
  • Analysis Commands / analys
  • Adaptive Poisson-Boltzmann Solver (APBS) / apbs
  • Atomic Solvation Parameter Based Energy / aspenr
  • Atomic Solvation Parameter Model with Implicit Membrane / aspenrmb
  • The AXD Module of CHARMM / axd
  • Partion molecular system into blocks / block
  • Combined Quantum Mechanical and Molecular Mechanics Method / cadpac
  • Common Component Architecture / cca
  • Consistent Force Field (CFF) / cff
  • CFTI: conformational energy/free energy calculations / cfti
  • CHARMM Developer's Change Log / changelog
  • Chemistry at HARvard Macromolecular Mechanics / charmm
  • CHARMM/POLYRATE INTERFACE / charmmrate
  • The CHarge EQuilibration Method / cheq
  • Using CMake to install CHARMM / cmake
  • CHARMM commands / commands
  • CONSTRAINTS / cons
  • Monte-carlo method for constant pH simulations / consph
  • The Coordinate Manipulation Commands / corman
  • Correlation Functions / correl
  • Solvent Correlation Functions / corsol
  • Reactive Molecular Dynamics with Surface Crossing / cross
  • Calculations on Crystals using CHARMM / crystl
  • Distributed CSA (Conformational Space Annealing) Command / csa
  • Distance Correlation (DCOR) / dcor
  • DENBIAS Module of CHARMM / denbias
  • CHARMM Developer Guide / developer
  • Combined Quantum Mechanical and Molecular Mechanics Method / diesel
  • How to set CHARMM to run with any size system / dimens
  • Dynamic Importance Sampling (DIMS) / dims
  • Domain Decomposition / domdec
  • Polarizable Drude Oscillator Format / drude
  • Dynamics: Description and Discussion / dynamc
  • Enveloping Distribution Sampling Method / eds
  • Effective Energy Function 1 / eef1
  • The EMAP module / emap
  • Energy Manipulations: Minimization and Dynamics / energy
  • ENSEMBLE averaging / replica exchange / ensemble
  • EPMF Module of CHARMM / epmf
  • The Ewald Summation method / ewald
  • FACTS: Fast Analytical Continuum Treatment of Solvation / facts
  • The Charge and Drude Polarizability Fitting / fitcharge
  • Parameter Fitting Procedure / fitparam
  • Combined QM/MM Fluctuating Charge Potential for CHARMM / flucq
  • Fast Multipole Method (FMM) for Nonbond Interactions / fmm
  • 4 Dimension dynamics: Description and Discussion / fourd
  • Up: (commands.doc) -=- Next: Syntax / fren
  • Combined Quantum Mechanical and Molecular Mechanics Method / g09
  • Galgor: Commands which deal with Genetic Algorithm and Monte Carlo. / galgor
  • Combined Quantum Mechanical and Molecular Mechanics Method / gamess
  • Combined Quantum Mechanical and Molecular Mechanics Method / gamess-uk
  • Gaussian Mixture Adaptive Umbrella Sampling (GAMUS) / gamus
  • Generalized Born Solvation Energy Module with Implicit Membrane / gbim
  • Generalized Born using Molecular Volume (GBMV) / gbmv
  • Generalized Born with a simple SWitching (GBSW) / gbsw
  • Generalized Born Solvation Energy and Forces Module / genborn
  • Genetic Neural Network / gnn
  • The Go pairwise Energy Module of CHARMM / gopair
  • Installing and running CHARMM on GPU / gpu
  • GRAPHICS / graphx
  • Grid: A general facility to implment grid-based potentials for docking / grid
  • Generation of Hydrogen Bonds / hbonds
  • Construction of hydrogen positions / hbuild
  • The HQBM Module of CHARMM / hqbm
  • IMAGES / images
  • CHARMM Release and Installation / install
  • The Internal Coordinate Manipulation Commands / intcor
  • Input-Output Commands / io
  • LARMORD: A Distance-based Chemical Shift Predictor / larmord
  • Lone Pair Facility / lonepair
  • Low Energy Path OPTmization / lupopt
  • Monte Carlo / mc
  • Monte Carlo Minimization/Annealing (MCMA) / mcma
  • Energy Manipulations: Minimization and Dynamics / minimiz
  • Miscellaneous Commands / miscom
  • Merck Molecular Force Field (MMFF94) / mmff
  • The MMFF94 Setup Procedure And Parameter Files / mmff_params
  • Miscellaneous mean field potentials / mmfp
  • Molecular Mechanics with Proton Transfer (MMPT) / mmpt
  • Combined Quantum Mechanical and Molecular Mechanics Method / mndo97
  • The MOLVIB Module of CHARMM / molvib
  • Monitor commands: Commands to monitor various dynamics properties / monitor
  • Multi-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) / mrmd
  • Multi-State Empirical Valence Bond / ms-evb
  • Multi Scale Command: MSCALE / mscale
  • Multipole Module / mtp
  • Spherical Multipole Electrostatic Module using Local / mtpl
  • Multiple Time Scales Method (MTS) / mts
  • Generation of Non-bonded Interactions / nbonds
  • NMR Analysis Module / nmr
  • The documentation of Nose-Hoover method - Masa Watanabe / nose
  • Combined Quantum Mechanical and Molecular Mechanics Method / nwchem
  • OpenMM GPU acceleration interface to CHARMM / openmm
  • Overlap of Molecular Similarity / overlap
  • Parallel Implementation of CHARMM / parallel
  • CHARMM Emprical Energy Function Parameters / parmfile
  • Poisson-Bolztmann Equation Module / pbeq
  • Details about TSM Free Energy Calculations / pdetail
  • Free Energy Perturbation Calculations / pert
  • Perturbation: Thermodynamic Perturbation Calculations. / perturb
  • Continuous constant pH Molecular Dynamics (PHMD) / phmd
  • Implementation of the Thermodynamic Simulation Method / pimplem
  • Polarizable Intermolecular Potential Functions (PIPF) / pipf
  • Plastic Network Model (PNM) / pnm
  • LIST OF ALL COMPILE (##) KEYWORDS IN CHARMM / preflx_list
  • CHARMM Preprocessing / prefx
  • Constant Pressure/Temperature (CPT) Dynamics / pressure
  • PRIMO Module of CHARMM / primo
  • Prototypes / proto
  • Combined Quantum Mechanical and Molecular Mechanics Method / qchem
  • Combined Quantum and Molecular Mechanical Hamiltonian / qmmm
  • A Quantum Mechanical / Molecular Mechanical (QM/MM) Interface / qturbo
  • Closed and Open Polymer Chain Path-Integral Methods for QM/MM / qub
  • Random Number Generator Controlling Commands / random
  • Residual Dipolar coupling (RDC) module / rdc
  • Radial Correlation Functions / rdfsol
  • The Parallel Distributed Replica / repdstr
  • Replica: Commands which deal with replication of the molecular system: Replica. / replica
  • RISM (Reference Interaction Site Model) module / rism
  • Residue Topology File / rtop
  • RUSH: A simple implicit-solvent force-field for protein simulation / rush
  • Rxncons: Commands for holonomic constrains of different order parameters / rxncons
  • The SASA implicit solvation model / sasa
  • Method and implementation of deformable boundary forces / sbound
  • SCALar : commands to manipulate scalar atom properties / scalar
  • Combined Quantum Mechanical and Molecular Mechanics Method / sccdftb
  • Screened Coulomb Potentials Implicit Solvent Model (SCPISM) / scpism
  • ATOM SELECTION / select
  • Self-Guided Langevin Dynamics (SGLD) / sgld
  • Shape Descriptors / shapes
  • Shell Decomposition / shell
  • Solid State NMR (SSNMR) Energy Functions / ssnmr
  • String method for the study of conformational transitions / stringm
  • Generation and Manipulation of the Structure (PSF) / struct
  • Command Line Substitution Parameters / subst
  • Support Programs and Data Files / support
  • Torsion Angle Molecular Dynamics (TAMD) Module / tamd
  • Test commands: Commands to test various conditions in CHARMM / test
  • CHARMM Testcases / testcase
  • Targeted Molecular Dynamics / tmd
  • Manipulating torques: TORQUE / torque
  • Temperature and pressure control / tpcntrl
  • Transition Path Sampling / tps
  • TReK: a program for Trajectory REfinement and Kinematics. / trek
  • Order Parameters / umbrel
  • How to use CHARMM / usage
  • VALBOND-TRANS / valbond
  • Vibration Analysis / vibran
  • The Z Module is a general facility for carrying out conformational / zerom